3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * GRoups of Organic Molecules in ACtion for Science
47 /* check kernel/toppush.c when you change these numbers */
49 #define MAXFORCEPARAM 12
53 typedef atom_id t_iatom;
55 /* this MUST correspond to the
56 t_interaction_function[F_NRE] in gmxlib/ifunc.c */
137 F_NRE /* This number is for the total number of energies */
142 /* Some parameters have A and B values for free energy calculations.
143 * The B values are not used for regular simulations of course.
144 * Free Energy for nonbondeds can be computed by changing the atom type.
145 * The harmonic type is used for all harmonic potentials:
146 * bonds, angles and improper dihedrals
148 struct {real a,b,c; } bham;
149 struct {real rA,krA,rB,krB; } harmonic;
150 struct {real lowA,up1A,up2A,kA,lowB,up1B,up2B,kB; } restraint;
151 /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
152 struct {real b0,kb,kcub; } cubic;
153 struct {real bm,kb; } fene;
154 struct {real r1e,r2e,krr; } cross_bb;
155 struct {real r1e,r2e,r3e,krt; } cross_ba;
156 struct {real theta,ktheta,r13,kUB; } u_b;
157 struct {real theta,c[5]; } qangle;
158 struct {real alpha; } polarize;
159 struct {real al_x,al_y,al_z,rOH,rHH,rOD; } wpol;
160 struct {real a,alpha1,alpha2,rfac; } thole;
161 struct {real c6,c12; } lj;
162 struct {real c6A,c12A,c6B,c12B; } lj14;
163 struct {real fqq,qi,qj,c6,c12; } ljc14;
164 struct {real qi,qj,c6,c12; } ljcnb;
165 /* Proper dihedrals can not have different multiplicity when
166 * doing free energy calculations, because the potential would not
167 * be periodic anymore.
169 struct {real phiA,cpA;int mult;real phiB,cpB; } pdihs;
170 struct {real dA,dB; } constr;
171 /* Settle can not be used for Free energy calculations of water bond geometry.
172 * Use shake (or lincs) instead if you have to change the water bonds.
174 struct {real doh,dhh; } settle;
175 /* No free energy supported for morse bonds */
176 struct {real b0,cb,beta; } morse;
177 struct {real pos0A[DIM],fcA[DIM],pos0B[DIM],fcB[DIM]; } posres;
178 struct {real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS]; } rbdihs;
179 struct {real a,b,c,d,e,f; } vsite;
180 struct {int n; real a; } vsiten;
181 /* NOTE: npair is only set after reading the tpx file */
182 struct {real low,up1,up2,kfac;int type,label,npair; } disres;
183 struct {real phi,dphi,kfac;int label,power; } dihres;
184 struct {int ex,power,label; real c,obs,kfac; } orires;
185 struct {int table;real kA;real kB; } tab;
186 struct {real sar,st,pi,gbr,bmlt; } gb;
187 struct {int cmapA,cmapB; } cmap;
188 struct {real buf[MAXFORCEPARAM]; } generic; /* Conversion */
191 typedef int t_functype;
194 * The nonperturbed/perturbed interactions are now separated (sorted) in the
195 * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
196 * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
208 * The struct t_ilist defines a list of atoms with their interactions.
209 * General field description:
211 * the size (nr elements) of the interactions array (iatoms[]).
213 * specifies which atoms are involved in an interaction of a certain
214 * type. The layout of this array is as follows:
216 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
217 * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
218 * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
220 * So for interaction type type1 3 atoms are needed, and for type2 and
221 * type3 only 2. The type identifier is used to select the function to
222 * calculate the interaction and its actual parameters. This type
223 * identifier is an index in a params[] and functype[] array.
228 real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
229 /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
234 int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
235 int grid_spacing; /* Grid spacing */
236 cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
244 t_functype *functype;
246 double reppow; /* The repulsion power for VdW: C12*r^-reppow */
247 real fudgeQQ; /* The scaling factor for Coulomb 1-4: f*q1*q2 */
248 gmx_cmap_t cmap_grid; /* The dihedral correction maps */
252 ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
259 t_functype *functype;
262 gmx_cmap_t cmap_grid;
263 t_iparams *iparams_posres;
264 int iparams_posres_nalloc;
271 * The struct t_idef defines all the interactions for the complete
272 * simulation. The structure is setup in such a way that the multinode
273 * version of the program can use it as easy as the single node version.
274 * General field description:
276 * defines the number of elements in functype[] and param[].
278 * the node id (if parallel machines)
280 * the number of atomtypes
281 * t_functype *functype
282 * array of length ntypes, defines for every force type what type of
283 * function to use. Every "bond" with the same function but different
284 * force parameters is a different force type. The type identifier in the
285 * forceatoms[] array is an index in this array.
287 * array of length ntypes, defines the parameters for every interaction
288 * type. The type identifier in the actual interaction list
289 * (ilist[ftype].iatoms[]) is an index in this array.
290 * gmx_cmap_t cmap_grid
291 * the grid for the dihedral pair correction maps.
292 * t_iparams *iparams_posres
293 * defines the parameters for position restraints only.
294 * Position restraints are the only interactions that have different
295 * parameters (reference positions) for different molecules
296 * of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
298 * The list of interactions for each type. Note that some,
299 * such as LJ and COUL will have 0 entries.
303 int n; /* n+1 is the number of points */
304 real scale; /* distance between two points */
305 real *tab; /* the actual tables, per point there are 4 numbers */